Merge pull request #1 from traitecoevo/skeleton

- Added rstan package infrastructure
- Added 1st precompiled linear model template
- Added more details in README
- Updated DESCRIPTION and NAMESPACE

.Rbuildignore

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+^rmot\.Rproj$
+^\.Rproj\.user$
+^README\.Rmd$

.gitignore

@@ -47,3 +47,4 @@ po/*~
 
 # RStudio Connect folder
 rsconnect/
+

DESCRIPTION

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+Package: rmot
+Title: What the Package Does (One Line, Title Case)
+Version: 0.0.0.9000
+Authors@R: 
+    person("First", "Last", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "YOUR-ORCID-ID"))
+Description: What the package does (one paragraph).
+License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
+    license
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
+Biarch: true
+Depends: 
+    R (>= 3.4.0)
+Imports: 
+    methods,
+    Rcpp (>= 0.12.0),
+    RcppParallel (>= 5.0.1),
+    rstan (>= 2.18.1),
+    rstantools (>= 2.3.1.1)
+LinkingTo: 
+    BH (>= 1.66.0),
+    Rcpp (>= 0.12.0),
+    RcppEigen (>= 0.3.3.3.0),
+    RcppParallel (>= 5.0.1),
+    rstan (>= 2.18.1),
+    StanHeaders (>= 2.18.0)
+SystemRequirements: GNU make

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(rmot_lm)
+import(Rcpp)
+import(methods)
+importFrom(RcppParallel,RcppParallelLibs)
+importFrom(rstan,sampling)
+importFrom(rstantools,rstan_config)
+useDynLib(rmot, .registration = TRUE)

R/rmot-package.R

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+#' The 'rmot' package.
+#'
+#' @description A DESCRIPTION OF THE PACKAGE
+#'
+#' @docType package
+#' @name rmot-package
+#' @aliases rmot
+#' @useDynLib rmot, .registration = TRUE
+#' @import methods
+#' @import Rcpp
+#' @importFrom rstan sampling
+#' @importFrom rstantools rstan_config
+#' @importFrom RcppParallel RcppParallelLibs
+#'
+#' @references
+#' Stan Development Team (NA). RStan: the R interface to Stan. R package version 2.26.23. https://mc-stan.org
+#'
+NULL

R/rmot_lm.R

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+#' Run a linear model in Stan
+#'
+#' @param x vector of numeric or integer predictor variable
+#' @param y vector of numeric or integer response variable
+#' @param ... additional arguments passed to rstan::sampling
+#'
+#' @return stanfit model output
+#' @export
+#'
+#' @examples
+#' mtcars
+#' rmot_lm(mtcars$mpg, mtcars$disp)
+rmot_lm <- function(x, y, ...) {
+  standata <- list(x = x, y = y, N = length(y))
+  out <- rstan::sampling(stanmodels$lm, data = standata, ...)
+  return(out)
+}

R/stanmodels.R

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+# Generated by rstantools.  Do not edit by hand.
+
+# names of stan models
+stanmodels <- c("lm")
+
+# load each stan module
+Rcpp::loadModule("stan_fit4lm_mod", what = TRUE)
+
+# instantiate each stanmodel object
+stanmodels <- sapply(stanmodels, function(model_name) {
+  # create C++ code for stan model
+  stan_file <- if(dir.exists("stan")) "stan" else file.path("inst", "stan")
+  stan_file <- file.path(stan_file, paste0(model_name, ".stan"))
+  stanfit <- rstan::stanc_builder(stan_file,
+                                  allow_undefined = TRUE,
+                                  obfuscate_model_name = FALSE)
+  stanfit$model_cpp <- list(model_cppname = stanfit$model_name,
+                            model_cppcode = stanfit$cppcode)
+  # create stanmodel object
+  methods::new(Class = "stanmodel",
+               model_name = stanfit$model_name,
+               model_code = stanfit$model_code,
+               model_cpp = stanfit$model_cpp,
+               mk_cppmodule = function(x) get(paste0("rstantools_model_", model_name)))
+})

README.Rmd

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+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  eval = FALSE,
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/README-",
+  out.width = "100%"
+)
+```
+
+# rmot
+
+<!-- badges: start -->
+<!-- badges: end -->
+
+The goal of 'rmot' is to ...
+
+## Installation
+
+You can install the development version of 'rmot' from [GitHub](https://github.com/) with:
+
+``` r
+# install.packages("remotes")
+remotes::install_github("traitecoevo/rmot")
+```
+
+## Demo
+
+```{r example}
+
+```

README.md

@@ -1 +1,20 @@
-# rmot
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# rmot
+
+<!-- badges: start -->
+<!-- badges: end -->
+
+The goal of ‘rmot’ is to …
+
+## Installation
+
+You can install the development version of ‘rmot’ from
+[GitHub](https://github.com/) with:
+
+``` r
+# install.packages("remotes")
+remotes::install_github("traitecoevo/rmot")
+```
+
+## Demo

Read-and-delete-me

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+Stan-specific notes:
+
+* All '.stan' files containing stanmodel definitions must be placed in 'inst/stan'.
+* Additional files to be included by stanmodel definition files
+  (via e.g., #include "mylib.stan") must be placed in any subfolder of 'inst/stan'.
+* Additional C++ files needed by any '.stan' file must be placed in 'inst/include',
+  and can only interact with the Stan C++ library via '#include' directives
+  placed in the file 'inst/include/stan_meta_header.hpp'.
+* The precompiled stanmodel objects will appear in a named list called 'stanmodels',
+  and you can call them with e.g., 'rstan::sampling(stanmodels$foo, ...)'

configure

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+#! /bin/sh
+
+# Generated by rstantools.  Do not edit by hand.
+
+"${R_HOME}/bin/Rscript" -e "rstantools::rstan_config()"

configure.win

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+#! /bin/sh
+
+# Generated by rstantools.  Do not edit by hand.
+
+"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "rstantools::rstan_config()"

inst/include/stan_meta_header.hpp

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+// Insert all #include<foo.hpp> statements here

inst/stan/include/license.stan

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+/*
+    rmot is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    rmot is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with rmot.  If not, see <http://www.gnu.org/licenses/>.
+*/

inst/stan/lm.stan

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+// A linear model
+data {
+  int<lower=1> N;
+  vector[N] x;
+  vector[N] y;
+}
+parameters {
+  real intercept;
+  real beta;
+  real<lower=0> sigma;
+}
+model {
+  // ... priors, etc.
+
+  y ~ normal(intercept + beta * x, sigma);
+}

rmot.Rproj

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+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+LineEndingConversion: Posix
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

src/Makevars

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+# Generated by rstantools.  Do not edit by hand.
+
+STANHEADERS_SRC = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "message()" -e "cat(system.file('include', 'src', package = 'StanHeaders', mustWork = TRUE))" -e "message()" | grep "StanHeaders")
+
+STANC_FLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "cat(ifelse(utils::packageVersion('rstan') >= '2.26', '-DUSE_STANC3',''))")
+PKG_CPPFLAGS = -I"../inst/include" -I"$(STANHEADERS_SRC)" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error $(STANC_FLAGS) -D_HAS_AUTO_PTR_ETC=0
+PKG_CXXFLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::CxxFlags()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::CxxFlags()")
+PKG_LIBS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::RcppParallelLibs()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::LdFlags()")
+
+CXX_STD = CXX17

src/RcppExports.cpp

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+// Generated by using Rcpp::compileAttributes() -> do not edit by hand
+// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#include <RcppEigen.h>
+#include <Rcpp.h>
+
+using namespace Rcpp;
+
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
+
+RcppExport SEXP _rcpp_module_boot_stan_fit4lm_mod();
+
+static const R_CallMethodDef CallEntries[] = {
+    {"_rcpp_module_boot_stan_fit4lm_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4lm_mod, 0},
+    {NULL, NULL, 0}
+};
+
+RcppExport void R_init_rmot(DllInfo *dll) {
+    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+    R_useDynamicSymbols(dll, FALSE);
+}

src/stanExports_lm.cc

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+// Generated by rstantools.  Do not edit by hand.
+
+#include <Rcpp.h>
+using namespace Rcpp ;
+#include "stanExports_lm.h"
+
+RCPP_MODULE(stan_fit4lm_mod) {
+
+
+    class_<rstan::stan_fit<stan_model, boost::random::ecuyer1988> >("rstantools_model_lm")
+
+    .constructor<SEXP,SEXP,SEXP>()
+
+
+    .method("call_sampler", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::call_sampler)
+    .method("param_names", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::param_names)
+    .method("param_names_oi", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::param_names_oi)
+    .method("param_fnames_oi", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::param_fnames_oi)
+    .method("param_dims", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::param_dims)
+    .method("param_dims_oi", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::param_dims_oi)
+    .method("update_param_oi", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::update_param_oi)
+    .method("param_oi_tidx", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::param_oi_tidx)
+    .method("grad_log_prob", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::grad_log_prob)
+    .method("log_prob", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::log_prob)
+    .method("unconstrain_pars", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::unconstrain_pars)
+    .method("constrain_pars", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::constrain_pars)
+    .method("num_pars_unconstrained", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::num_pars_unconstrained)
+    .method("unconstrained_param_names", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::unconstrained_param_names)
+    .method("constrained_param_names", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::constrained_param_names)
+    .method("standalone_gqs", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::standalone_gqs)
+    ;
+}